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DOE OSTI2025

Phosphoproteomics Modifications in Women with Rheumatoid Arthritis─Application of Web-Based Software to Enhance Data Visualization

Individuals with rheumatoid arthritis (RA) are at increased risk of functional disability, cardiovascular disease, and obesity, all of which are influenced by dysregulated skeletal muscle. Here, this pilot study aims to identify phosphoproteomics changes in RA skeletal muscle and visualize modifications through development of a web-based app designed to promote user-friendly data interpretation and visualization. NanoLC–MS/MS analysis was performed on vastus lateralis biopsies from three women with RA and matched healthy controls. Differential analysis was performed using the Limma R package. Kinase substrate enrichment analysis (KSEA) predicted changes in kinase activity. RA muscle displayed 35 upregulated and 60 downregulated phosphosites, including the cytoskeletal proteins TTN (Ser33201, Ser33013, Ser20925), NEB (Ser2219, Thr254, Ser33013, Ser20925), FLNA (Ser1459), and LASP1 (Ser146). Compared to healthy controls, KSEA predicted decreased activity of several kinases in RA muscle, including PRKACA and CDKs. All such changes were visualized by use of our web-based app. Overall, phosphoproteome analysis reveals signaling alterations in RA skeletal muscle linked to cytoskeletal proteins, representing candidate disease biomarkers; these modifications can be explored through use of our web-based software.

phosphoproteomics↗

DOE OSTI2023

Three-dimensional phenotyping of peach tree-crown architecture utilizing terrestrial laser scanning

Tree training systems for temperate fruit have been developed throughout history by pomologists to improve light interception, fruit yield, and fruit quality. These training systems direct crown and branch growth to specific configurations. Quantifying crown architecture could aid the selection of trees that require less pruning or that naturally excel in specific growing/training system conditions. Regarding peaches [Prunus persica (L.) Batsch], access tools such as branching indices have been developed to characterize tree-crown architecture. However, the required branching data (BD) to develop these indices are difficult to collect. Traditionally, BD have been collected manually, but this process is tedious, time-consuming, and prone to human error. These barriers can be circumnavigated by utilizing terrestrial laser scanning (TLS) to obtain a digital twin of the real tree. TLS generates three-dimensional (3D) point clouds of the tree crown, wherein every point contains 3D coordinates (x, y, z). To facilitate the use of these tools for peach, we selected 16 young peach trees scanned in 2021 and 2022. These 16 trees were then modeled and quantified using the open-source software TreeQSM. As a result, “in silico” branching and biometric data for the young peach trees were calculated to demonstrate the capabilities of TLS phenotyping of peach tree-crown architecture. The comparison and analysis of field measurements (in situ) and in silico BD, biometric data, and quantitative structural model branch uncertainty data were utilized to determine the reconstructive model’s reliability as a source substitute for field measurements. Mean average deviation when comparing young tree (YT) height was approx. 5.93%, with crown volume was approx. 13.26% across both 2021 and 2022. All point clouds of the YTs in 2022 showed residuals lower than 12 mm to cylinders fitted to all branches, and mean surface coverage greater than 40% for both the trunk and primary branching orders.

09 BIOMASS FUELS↗

DOE OSTI2020

PyXAS – an open-source package for 2D X-ray near-edge spectroscopy analysis

In the synchrotron X-ray community, X-ray absorption near-edge spectroscopy (XANES) is a widely used technique to probe the local coordination environment and the oxidation states of specific elements within a sample. Although this technique is usually applied to bulk samples, the advent of new synchrotron sources has enabled spatially resolved versions of this technique (2D XANES). This development has been extremely powerful for the study of heterogeneous systems, which is the case for nearly all real applications. However, associated with the development of 2D XANES comes the challenge of analyzing very large volumes of data. As an example, a single 2D XANES measurement at a synchrotron can easily produce ~106 spatially resolved XANES spectra. Conventional manual analysis of an individual XANES spectrum is no longer feasible. Here, a software package is described that has been developed for high-throughput 2D XANES analysis. A detailed description of the software as well as example applications are provided.

25 ENERGY STORAGE↗

DOE OSTI2022

The SODA Approach: Leveraging High-Level Synthesis for Hardware/Software Co-design and Hardware Specialization: Invited

Novel "converged" applications combine phases of scientific simulation with data analysis and machine learning. Each computational phase can benefit from specialized accelerators. However, algorithms evolve so quickly that mapping them on existing accelerators is suboptimal or even impossible. This paper presents the SODA (Software Defined Accelerators) framework, a modular, multi-level, open-source, no-human-in-the-loop, hardware synthesizer that enables end-to-end generation of specialized accelerators. SODA is composed of SODA-Opt, a high-level frontend developed in MLIR that interfaces with domain-specific programming frameworks and allows performing system level design, and Bambu, a state-of-the-art high-level synthesis engine that can target different device technologies. The framework implements design space exploration as compiler optimization passes. We show how the modular, yet tight, integration of the high-level optimizer and lower-level HLS tools enables the generation of accelerators optimized for the computational patterns of converged applications. We then discuss some of the research opportunities that such a framework allows, including system-level design, profile driven optimization, and supporting new optimization metrics.

Bohm Agostini, Nicolas↗

DOE OSTI2022

AutodiDAQt v1.1.0

AutodiDAQt automates and simplifies writing data acquisition software for spectroscopy and microscopy. After defining only how to communicate with instruments and hardware, autodiDAQt generates user interfaces for long running acquisition applications, handlings data collation and retention, and provides remote communication to analysis computers. This reduces the time to get experiments running from months to hours and increases reliability for scientific experiments. AutodiDAQt metaprograms from instrument drivers directly, where possible.

Stansbury, Conrad↗

DOE OSTI2025

EV-ELM (Electric Vehicle Policies with the Energy Language Model) [SWR-25-156]

Electric Vehicle Policies with the Energy Language Model (EV-ELM) leverages previous work using Large Language Models (LLMs) to find, download, and parse policy information related to energy infrastructure. In this application, we use LLMs to find policy documents related to the permitting and installation of electric vehicle charging infrastructure. This software contains the code to find, download, and parse these documents, while a related data record in the Open Energy Data Initiative (OEDI) will include the resulting output dataset that can be used for downstream analysis. The EV-ELM repository contains code for the EV-ELM project, which focuses on retrieving and processing EV permitting processes using large language models. The project is composed of two pipelines: (1) a web scraping pipeline for discovering and downloading EV permitting documents, and (2) a document parsing and extraction pipeline that processes the downloaded files to produce structured data. The web scraping pipeline is designed to extract relevant information from various websites, while the document parsing pipeline processes and analyzes the extracted documents to derive meaningful insights. Both pipelines depend on the NLR elm repository, which provides essential tools and functionalities for handling and processing the data. The web scraping pipeline is a modified version of the ordinance_gpt example within the elm repository. It has been adapted to fit the specific requirements of the EV-ELM project, ensuring that it effectively captures and processes the necessary information related to EV permitting.

Olson, Reid [National Laboratory of the Rockies (N↗

DOE OSTI2020

Composite Analysis Solid Waste Release Data Reduction of Activity Flux from Waste Sites to the Vadose Zone for Baseline Assessment

This environmental calculation file (ECF) describes the data reduction methodology for the solid waste release datasets generated by the Composite Analysis Solid Waste Release (CASWR) model (CP-62766, Model Package Report: Composite Analysis Solid Waste Release Model [CASWR Model]) and documents the resulting reduced datasets for the updated Composite Analysis (CA) baseline assessment. This ECF is in support of the updated Hanford Site CA. The purpose of the updated Hanford Site CA is to provide an estimate of the cumulative radiological impacts from active and planned low-level radioactive waste disposals and other potentially interacting radioactive waste disposal sources that will remain following Hanford Site closure. The vadose zone modeling activities associated with the CA includes solid waste forms as contaminant sources. To support the modeling of solid waste transport from the vadose zone to the groundwater at the Hanford Site, the CASWR model was designed to generate deterministic radionuclide release rates for the Hanford Site Central Plateau solid waste disposal sites. The complete CASWR model-generated dataset for the CA Baseline Assessment consists of 2,378,831 sets of time and release rates (1,073,869 sets for the 200 East Area and 1,304,962 sets for the 200 West Area), representing a course of the simulation from year 1953 to year 12,069, 16 radiological contaminants of potential concern (COPCs), and 237 solid waste sources as documented in ECFHANFORD- 19-0112, Solid Waste Release Calculations for the Composite Analysis Baseline Assessment. For several of the STOMP vadose zone models, the number of release rate data pairs required for release at all waste sites would exceed the limitations imposed by the STOMP modelling software package used to simulate contaminant transport through the vadose zone. As a result, a data reduction of the CASWR dataset is required prior to its use as a source input for the CA vadose zone modeling activities.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Fermilab Italian Student Program (Final Report)

I participated to the 2019 Fermilab Italian Student Program under the supervision of Anadi Canepa and Lorenzo Uplegger. I worked with the Fermilab research group that is involved with the R&D of the CMS Outer Tracker. The Compact Muon Solenoid (CMS) is a a general-purpose detector located at the Large Hadron Collider (LHC), the world's most powerful particle accelerator. In the next years LHC will undergo the High-Luminosity LHC upgrade, which will bring its luminosity from 1 × 10 34 cm -2 s -1 to 1.5 × 10 34 cm -2 s -1 . This increase in luminosity will require an upgrade of CMS as well, in order to comply with the augmented rate of particles which will cross the detector. The CMS tracker is a detector, composed of various modules made of silicon pixel trackers and silicon strip trackers, whose aim is to reconstruct the trajectories of the particles produced by the collisions in LHC. The tracker is ideally divided in Inner Tracker and Outer Tracker. The HL-LHC upgrade put important challenges in the designing of the tracker. It will have to withstand the irradiation of a large fluence of particles, without suffering a too severe deterioration of its performance. In addition to this, in order to comply with the increased rate of events that CMS will need to detect, the tracker will be exploited for triggering at the fully hardware Level 1 Trigger, in contrast to the current tracker, whose data are only used for the software High-Level Trigger. This feature is managed by the "stub logic", which will be explained in chapter 2. During the months of August and September at Fermilab I carried out the data analysis of three test beam runs performed in the last two years on the 2S Outer Tracker Minimules. The 2S Minimoule consists of two silicon strip trackers placed one upon the other with the strips kept parallel.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Search for Joint Multimessenger Signals from Potential Galactic Cosmic-Ray Accelerators with HAWC and IceCube

The origin of high-energy galactic cosmic rays is yet to be understood, but some galactic cosmic-ray accelerators can accelerate cosmic rays up to PeV energies. The high-energy cosmic rays are expected to interact with the surrounding material or radiation, resulting in the production of gamma-rays and neutrinos. To optimize for the detection of such associated production of gamma-rays and neutrinos for a given source morphology and spectrum, a multimessenger analysis that combines gamma-rays and neutrinos is required. In this study, we use the Multi-Mission Maximum Likelihood framework with IceCube Maximum Likelihood Analysis software and HAWC Accelerated Likelihood to search for a correlation between 22 known gamma-ray sources from the third HAWC gamma-ray catalog and 14 yr of IceCube track-like data. No significant neutrino emission from the direction of the HAWC sources was found. We report the best-fit gamma-ray model and 90% CL neutrino flux limit from the 22 sources. From the neutrino flux limit, we conclude that, for five of the sources, the gamma-ray emission observed by HAWC cannot be produced purely from hadronic interactions. We report the limit for the fraction of gamma-rays produced by hadronic interactions for these five sources.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

PROTOCALC, a W -band Polarized Calibrator for Cosmic Microwave Background Telescopes: Application to Simons Observatory and CLASS

Current- and next-generation cosmic microwave background (CMB) experiments will measure polarization anisotropies with unprecedented sensitivities. The need for high precision in these measurements underscores the importance of gaining a comprehensive understanding of instrument properties, with a particular emphasis on the study of the beam properties, and especially their polarization characteristics and the measurement of the polarization angle. In this context, a major challenge lies in the scarcity of millimeter polarized astrophysical sources with sufficient brightness and calibration knowledge to meet the stringent accuracy requirements of future CMB missions. This led to the development of a drone-borne calibration source designed for the frequency band centered on approximately 90 GHz, matching a commonly used channel in ground-based CMB measurements. The Prototype Calibrator for Cosmology, PROTOCALC, has undergone thorough in-lab testing, and its properties have been subsequently modeled through simulation software integrated into the standard Simons Observatory analysis pipeline. Moreover, the PROTOCALC system has been tested in the field, having been deployed twice on calibration campaigns with CMB telescopes in the Atacama Desert. The data collected constrain the roll angle of the source with a statistical accuracy of 0$^°_•$045.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Oklo Sponsored Testing using PELICAN: System, Subchannel, and High-Fidelity Software Validation (Final CRADA Report)

Argonne National Laboratory (the Contractor), located in Lemont IL, and Oklo, Inc., (the Participant), headquartered in Santa Clara, CA, propose to enter into a Cooperative Research and Development Agreement (CRADA) to perform a gap analysis of thermal hydraulic data, perform prototypical fuel assembly pressure drop and cavitation model validation, generate the experimental data as well as the corresponding uncertainties for this matrix and, finally, develop the validation models with the Argonne system level code SAS4A/SASSYS-1, the Argonne subchannel analysis code DASSH, the Argonne high fidelity code Nek5000, and/or the Idaho National Laboratory code Pronghorn Subchannel. The work outlined below will significantly improve the experimental and validation database currently available for liquid metal fast reactors, thus making it a viable part of a comprehensive reactor design and licensing suite to be used by the participant.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

libwfa: Wavefunction analysis tools for excited and open‐shell electronic states

Abstract An open‐source software library for wavefunction analysis, libwfa, provides a comprehensive and flexible toolbox for post‐processing excited‐state calculations, featuring a hierarchy of interconnected visual and quantitative analysis methods. These tools afford compact graphical representations of various excited‐state processes, provide detailed insight into electronic structure, and are suitable for automated processing of large data sets. The analysis is based on reduced quantities, such as state and transition density matrices (DMs), and allows one to distill simple molecular orbital pictures of physical phenomena from intricate correlated wavefunctions. The implemented descriptors provide a rigorous link between many‐body wavefunctions and intuitive physical and chemical models, for example, exciton binding, double excitations, orbital relaxation, and polyradical character. A broad range of quantum‐chemical methods is interfaced with libwfa via a uniform interface layer in the form of DMs. This contribution reviews the structure of libwfa and highlights its capabilities by several representative use cases. This article is categorized under: Software > Quantum Chemistry Theoretical and Physical Chemistry > Spectroscopy

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Implementation of high-speed data acquisition at DIII-D

Research at the DIII-D National Fusion Facility in San Diego focuses on short pulse plasma discharges that specialize on various shaping profiles. High-speed data collection is a critical component for the operation of many of DIII-D’s diagnostics and is fundamental for capturing high-resolution data used in experimental data analysis. Differing techniques enable the plasma control system (PCS) to perform complex real-time feedback control on microsecond time scales. This work presents a comprehensive overview of data acquisition, focusing on the hardware and software used in reliable data acquisition at DIII-D. The robust nature of the data acquisition system allows for various techniques to coexist seamlessly. However, as modern systems capable of nanosecond resolution become more common, existing architectures will need to be modified. Here, by addressing the key challenges of high-speed data acquisition, DIII-D is able to provide real-time data used in plasma operation and has the ability to acquire high fidelity data needed for future experimental fusion reactors, such as ITER.

Control↗

DOE OSTI2023

Rovibronic molecular line list for the $N_2(C^3Π_u–B^3Π_g)$ second positive system

Here, a line list for the N second positive system, $B^3Π_g—C^3Π_u$, has been compiled using the PGOPHER spectral simulation software. The line list extends the number of vibrational states of the $B^3Π_g$ up to v=29 and a maximum rotational state of J=150 for simulation temperatures up to 7000 K. New electronic–vibrational transition moments were calculated using refined potential energy curves and a transition dipole moment with the DUO software. Comparisons to experimental data and the SPECAIR software have been used to validate the new line list. The results are available in ASCII ExoMol .state and .trans files and as a PGOPHER input file for use in spectral analysis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Digital Twin for Chemical Science (DTCS) v0.01

Directly visualizing the trajectories of chemistry can unravel novel insights into the behavior of catalysts, gas phase reactions, photo-induced dynamics, and building blocks for quantum information processing. The ability of explicitly identifying, tracking, and tagging the exchange of matter, hence the annihilation and creation of new chemical species, can be best realized through a close coupling of theory and experiment. While the synchrotron-based characterization facilities propelled rapidly in its hardware, providing higher brightness, better resolution, and more precision, the software infrastructure is lagging. We developed DTCS (Digital Twin for Chemical Science) v.01, a central platform that faithfully mimics advanced instrumentations in Scientific User Facilities, by solving a variety of technical challenges in data acquisition, analysis, and model-driven interpretation. Rooted in physics and accelerated by AI, we validated this concept by direct comparison with precise experimental X-ray Photoelectron Spectroscopy (XPS) observations using a ubiquitous metal-water interfacial scenario, i.e., Ag/H2O as our main narrative. The DTCS v.01 input mirrors how the bench chemists work, with the output directly linked to the end station computer, thereby providing a user-friendly, knowledge-driven, and accessible user experience with mechanistic insights standardized in a way that are ready to be published, versioned, and transferred flexibly.

Qian, Jin↗

DOE OSTI2022

Detector Simulation Challenges for Future Accelerator Experiments

Detector simulation is a key component for studies on prospective future high-energy colliders, the design, optimization, testing and operation of particle physics experiments, and the analysis of the data collected to perform physics measurements. This review starts from the current state of the art technology applied to detector simulation in high-energy physics and elaborates on the evolution of software tools developed to address the challenges posed by future accelerator programs beyond the HL-LHC era, into the 2030–2050 period. New accelerator, detector, and computing technologies set the stage for an exercise in how detector simulation will serve the needs of the high-energy physics programs of the mid 21st century, and its potential impact on other research domains.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Pele: An Exascale-Ready Suite of Combustion Codes

High fidelity simulations of realistic combustion devices are extremely demanding computationally because of the requirements to capture complex fuel chemical decomposition, its intricate interactions with turbulent, often multiphase, flows, and the wide separation of space and time scales between the thin flame and the device boundaries. Software required to carry out such computations tends to be extremely complex, particularly when designed to exploit hardware accelerators, and can be difficult to port and maintain. We present Pele, a performance portable suite of tools for the simulation of combustion systems, including codes to evolve reactive multiphase configurations in the low Mach number and compressible flow regimes, along with a set of inter-compatible post processing and in situ analysis tools. The Pele suite of tools is built on top of the AMReX framework for block-structured adaptive mesh refinement, which provides efficient data structures and algorithms that enable the development of a wide variety of efficient mesh and particle based PDE integration schemes. A hierarchical MPI+X parallelism scheme supports CPU-only and accelerated architectures, where X can be OpenMP, CUDA, and HIP based approaches for intra-node computational work distribution. The algorithms and data structures underlying the Pele simulation and analysis tools are highly scalable and performant across a wide variety of high-performance computing platforms, including DOEs newest exascale-class machines, Frontier and Aurora. The simulation and analysis tools are fully documented and freely distributed as open source via GitHub. We present key algorithmic and software challenges, solution strategies, performance and resulting set of capabilities.

AMReX↗

DOE OSTI2020

BASS: An R Package for Fitting and Performing Sensitivity Analysis of Bayesian Adaptive Spline Surfaces

In this work, we present the R package BASS as a tool for nonparametric regression. The primary focus of the package is fitting fully Bayesian adaptive spline surface (BASS) models and performing global sensitivity analyses of these models. The BASS framework is similar to that of Bayesian multivariate adaptive regression splines (BMARS) from Denison, Mallick, and Smith (1998), but with many added features. The software is built to efficiently handle significant amounts of data with many continuous or categorical predictors and with functional response. Under our Bayesian framework, most priors are automatic but these can be modified by the user to focus on parsimony and the avoidance of overfitting. If directed to do so, the software uses parallel tempering to improve the reversible jump Markov chain Monte Carlo (RJMCMC) methods used to perform inference. We discuss the implementation of these features and present the performance of BASS in a number of analyses of simulated and real data.

97 MATHEMATICS AND COMPUTING↗